Management Topics

Sep 21, 2012

Breed update on genomically-enhanced EPDs

All the news of late on the EPD (expected progeny difference) front has been about the advances in genomics technology. Many of the larger breeds are moving extremely rapidly at incorporating genomics in order to make their EPDs more accurate, especially earlier in an animal’s life. The hope is to benefit producers in allowing them to make better selection decisions. I will first make a very simplistic overview of genomics and then discuss where some of the larger breeds are in working with it.

Most everybody is familiar with DNA, the basic coding for life. Genomics is just a fancy word for finding places that are informative on areas of DNA for certain traits. The technology first used was markers, which is essentially identifying a place on the DNA that was closely associated with the area or gene of interest. This was cumbersome and only left us with markers for a few traits. Today, instead of looking at a few markers, the industry has moved on to SNPs (single nucleotide polymorphisms). In a nutshell, this allows the industry to look at a wholesale number of the most basic elements that make up DNA on a high density SNP panel (up to 50,000 SNPs compose a panel, i.e. 50K) to find a large number of SNPs that explain variation for any number of traits. With this newer technology, the barn doors were opened for genomically-enhanced EPDs for all traits.

Now let’s take a look at where the 10 largest breeds are in incorporating the SNP technology:

Angus—American Angus Association’s wholly owned subsidiary AGI (Angus Genetics Incorporated) produces a genetic analysis in house. One of their biggest achievements in 2009 was the release of genomically-enhanced EPDs. Although genomics were first used just on carcass traits, they quickly expanded, so in the fall of 2011, all traits were genomically enhanced. Unlike most breeds that currently single-source their panels, AGI accepts data from multiple labs.

Hereford—American Hereford Association has 50K data on about 1,200 influential sires allowing them to calculate genomically-enhanced EPDs. However, the vendor they use to calculate their EPDs, the Agricultural Business Research Institute’s (ABRI) Breedplan in Australia, is not ready to incorporate them into the analysis. Therefore, they started in the summer of 2012 an interim regime to increase accuracies on an individual, but this regime has the downside of not enhancing the accuracies of the other animals in the pedigree.

Charolais—The American International Charolais Association works with AGI and currently has the goal of collecting and analyzing 1,000 head for 50K SNP panel, but is not close to implementation.

Simmental—American Simmental Association (ASA) pioneered the use of markers in 2005 by incorporating a shear force marker into the first genomically-enhanced EPD: tenderness.

It was second after Angus, implementing genomically-enhanced EPDs on its full suite of EPDs in the spring of 2012. ASA also pioneered the use of genomics with hybrids as it has been assumed that the technology was for purebreds only. ASA does its analysis in-house with Red Angus.

Red Angus—The Red Angus Association of America (RAAA) collected a large number of 50K samples, creating a training population and calculated parameters that will allow it to have genomically-enhanced EPDs in the next genetic evaluation. Prior to any EPD release, especially one with a new calculation, the genetic prediction(s) must be given the okay by an outside technical committee. RAAA does a joint ASA/ RAAA evaluation.

Gelbvieh—With over 800 samples, they continue to gather 50K samples while simultaneously doing training analysis at Iowa State University (ISU). The American Gelbvieh Association works with AGI and hopes to have genomically-enhanced EPDs between this winter and next summer.

Brangus—The International Brangus Breeders Association (IBBA) currently has a large number (1,400) of both 50K and some 700K samples. They have the challenge of dealing with a breed that is a combination of Bos Taurus and Bos Indicus. Therefore, they are doing discovery for a within-breed solution with ISU and an across-breed solution with Geneseek. IBBA does its analysis with the University of Georgia.

Limousin—NALF (North American Limousin Foundation) was fortunate that it had a large number of samples at the University of Missouri on file from a previous test for a genetic defect that a researcher had used in his 50K SNP work. This got them off to a quick start at little investment. With purebreds done, they are now working on shoring up their hybrids, and the plan is to have genomically-enhanced EPDs in their next genetic analysis with AGI.

Beefmaster—Beefmaster Breeders United (BBU) has chosen to focus its resources on describing the “5 Essentials,” upon which the breed is based, with EPDs rather than spending those resources on genomics. BBU does its analysis with ABRI.

Shorthorn—The American Shorthorn Association is taking a slow and steady approach to genomics, and is currently working on putting together a training population. They do their analysis with Colorado State University. — Dr. Bob Hough

[Dr. Bob Hough has served as the executive vice president of the Red Angus Association of American and more recently as executive vice president of the North American Limousin Foundation from 2009 to early 2011. He is now a consultant, freelance writer and semiretired.]